The HIAPER Project Office (HPO) was a part of the NCAR Directorate. As such, the HPO director, Krista Laursen, reported to Tim Killeen, the Director of NCAR. General oversight was provided by the University Corporation for Atmospheric Research (UCAR), through its president, Rick Anthes. This structure is represented graphically as follows:

In addition to this formal organizational structure, ongoing interaction existed between the HPO and the HIAPER Integrated Project Team (HIPT), a group of UCAR, NCAR and NSF staff involved with HIAPER who met by telephone conference call as needed to discuss the status of the project and to review upcoming plans, goals and objectives. The NSF HIAPER Program Official, James Huning, was a member of the HIPT.

The HPO established Integrated Project Team (IPT) subgroups to focus on and advise the HPO about developments and critical HIAPER tasks related to various infrastructure, instrumentation and aircraft operation categories. The subgroup co-chairs and members interface with the HPO on a regular basis and worked with Project Office staff to plan, schedule, and complete the various infrastructure and scientific measurement tasks critical to bringing the aircraft on-line.

Scientific guidance and input to the project was provided by the HIAPER Advisory Committee (HAC), which was advisory to the NCAR Director. The members of the HAC were drawn from universities, NOAA, NASA, NCAR and NSF. The HAC was charged with guiding the HIAPER project in directions that ensured maximum benefit of the program to the scientific community. The HAC also ensured effective community involvement in the HIAPER acquisition and in the modifications to and instrumentation of the platform.

Once HIAPER became fully operational in late 2005 (see the HIAPER Timeline for more information), the Observing Facilities Allocation Panel (OFAP) and the Facilities Allocations Committee (FAC) assumed responsibility for reviewing proposals for its use, and making allocation decisions for usage of the GV.